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Monday, December 2, 2019

Representing (& graphing) the root edge of a tree as an additional unbranching edge

Yesterday a phytools user complained on Twitter that phytools::plotTree
could not plot a root edge:

Wow, the interfaces to draw trees in base R are so unintuitive. Ape's plot.phylo() doesn't align the y-axis such that zero is where tips begin with. phytools plotTree() does, but won't draw the root edge and has little options.

About this blog

This web-log chronicles the development of new tools for phylogenetic analyses in the phytools R package. Unless you a reading a very recent page of the blog, I recommend that you install the latest CRAN version of phytools (or latest beta release) before attempting to replicate any of the analyses of this site. That is because the linked functions may be archived, and very likely have been replaced by newer versions.